Publications related to A method and system to build an ir fingerprint database for the structural identification of biomolecules

Related publications (19)

Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak

Yury Tsybin, Natalia Gasilova, Laure Menin, Anton Kozhinov, Konstantin Nagornov

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for ...

Amer Chemical Soc2024

Gradients of Deposition and In Situ Production Drive Global Glacier Organic Matter Composition

Tom Ian Battin, Hannes Markus Peter, Matteo Tolosano, Vincent Henri De Staercke, Michail Styllas, Martina Andrea Schön

Runoff from rapidly melting mountain glaciers is a dominant source of riverine organic carbon in many high-latitude and high-elevation regions. Glacier dissolved organic carbon is highly bioavailable, and its composition likely reflects internal (e.g., aut ...

2024

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

Direct observation of glycans bonded to proteins and lipids at the single-molecule level

Klaus Kern, Stephan Rauschenbach

Proteins and lipids decorated with glycans are found throughout biological entities, playing roles in biological functions and dysfunctions. Current analytical strategies for these glycan-decorated biomolecules, termed glycoconjugates, rely on ensemble-ave ...

American Association for the Advancement of Science2023

Combining multi-stage ion mobility spectrometry with cryogenic infrared spectroscopy for glycan analysis

Priyanka Bansal

Structural analysis of biomolecules is essential to understanding biological processes. Among the various classes of biomolecules, glycans have gained significant attention recently due to their ubiquitous roles in biological systems. However, study of gly ...

EPFL2022

Characterization of the Time-Domain Isotopic Beat Patterns of Monoclonal Antibodies in Fourier Transform Mass Spectrometry

Natalia Gasilova, Laure Menin

The time-domain transients in the Fourier transform mass spectrometry (FTMS) analysis of monoclonal antibodies (mAbs) are known to exhibit characteristic isotopic beat patterns. These patterns are defined by the isotopic distributions of all gaseous mAb io ...

2022

Molecular Vibration Explorer: an Online Database and Toolbox for Surface-Enhanced Frequency Conversion and Infrared and Raman Spectroscopy

Christophe Marcel Georges Galland

We present Molecular Vibration Explorer, a freely accessible online database and interactive tool for exploring vibrational spectra and tensorial lightvibration coupling strengths of a large collection of thiolated molecules. The "Gold" version of the data ...

AMER CHEMICAL SOC2022

Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study

Eduardo Carrascosa Casado

The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric i ...

AMER CHEMICAL SOC2021

Analyzing glycans cleaved from a biotherapeutic protein using a combination of ion mobility spectrometry and cryogenic ion spectroscopy

Natalia Yalovenko

The characterization of biomolecules plays a central role in biomedical research. The development of state-of-the-art technologies is needed to make such analyses faster, more sensitive, and more accurate. While mass spectrometry continues to play a centra ...

EPFL2021

Spatially-distributed cyclotron oscillators approach to FT-ICR MS at the true cyclotron frequency: Computational evaluation of sensitivity

Yury Tsybin, Anton Kozhinov, Konstantin Nagornov

Routine Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with ion detection at the unreduced (true) cyclotron frequency, instead of the reduced cyclotron frequency, has recently been demonstrated experimentally and supported computat ...

ELSEVIER2021

CO2 Hydrogenation over Unsupported Fe-Co Nanoalloy Catalysts

Andreas Züttel, Kun Zhao, Robin Tobias Andreas Mutschler, Marco Calizzi

The thermo-catalytic synthesis of hydrocarbons from CO2 and H2 is of great interest for the conversion of CO2 into valuable chemicals and fuels. In this work, we aim to contribute to the fundamental understanding of the effect of alloying on the reaction y ...

2020

Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion Mobility Spectrometry and Cryogenic Ion Spectroscopy

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Valeriu Scutelnic

The analysis of carbohydrates, or glycans, is challenging for established structure-sensitive gas-phase methods. The multitude of possible stereo-, regio- and structural isomers make them substantially more complex to ana-lyze than DNA or proteins, and no ...

2019

Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev

Identification of isomeric amino acid residues in peptides and proteins is challenging but often highly desired in proteomics. One of the practically important cases that require isomeric assignments is that associated with single-nucleotide polymorphism s ...

AMER CHEMICAL SOC2019

Development of mass spectrometric methods to understand the mechanism of action of transition metal-based anticancer compounds

Fook Seng Ronald Lee

Metal based anti-cancer drugs (metallodrugs) such as cisplatin are a cornerstone of cancer chemotherapy. However, development of this class of compound has been hindered by our lack of understanding of how they function. This is mainly because existing met ...

EPFL2016

Soft-landing electrospray ion beam deposition of sensitive oligoynes on surfaces in vacuum

Klaus Kern, Holger Frauenrath, Stephan Rauschenbach, Stephen Schrettl, Gordon Rinke, Tobias Hoheisel

Characterizing the complex structure of such molecules with highly resolving, vacuum-based methods like scanning probe microscopy requires their transfer into the gas phase and further onto an atomically clean surface in ultrahigh vacuum without causing ad ...

Elsevier2015

Fragmentation mechanism of UV-excited peptides in the gas phase

Thomas Rizzo, Oleg Boyarkine, Michael Zachary Kamrath, Aleksandra Zabuga

We present evidence that following near-UV excitation, protonated tyrosine- or phenylalanine–containing peptides undergo intersystem crossing to produce a triplet species. This pathway competes with direct dissociation from the excited electronic state and ...

American Institute of Physics2014

Top-down and middle-down mass spectrometry structural characterization of monoclonal antibodies

Luca Fornelli

EPFL2014

Iterative Method for Mass Spectra Recalibration via Empirical Estimation of the Mass Calibration Function for Fourier Transform Mass Spectrometry-Based Petroleomics

Yury Tsybin, Anton Kozhinov, Konstantin Zhurov

We describe a mass spectra recalibration method, which enables analysis of petroleum samples with Orbitrap FTMS. In this method, the mass calibration function is estimated on the basis of mass-to-charge ratios and abundances of internal calibrants without ...

Amer Chemical Soc2013

Practical Considerations for Improving the Productivity of Mass Spectrometry-based Proteomics

Yury Tsybin, Anton Kozhinov, Luca Fornelli, Kristina Srzentic, Unige Anna Laskay

Mass spectrometry (MS) is currently the most sensitive and selective analytical technique for routine peptide and protein structure analysis. Top-down proteomics is based on tandem mass spectrometry (MS/MS) of intact proteins, where multiply charged precur ...

Schweizerische Chemische Gesellschaft2013